ArticleProceedings. Biological sciences2014
Two-phase importance sampling for inference about transmission trees.
Article in Proceedings. Biological sciences, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- A Bayesian inference method to estimate transmission trees with multiple introductions; applied to SARS-CoV-2 in Dutch mink farms.PLoS computational biology · 2023Article
- Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review.Pathogens (Basel, Switzerland) · 2022Review
- Bayesian reconstruction of transmission trees from genetic sequences and uncertain infection times.Statistical applications in genetics and molecular biology · 2020Article
- The spread of a wild plant pathogen is driven by the road network.PLoS computational biology · 2020Article
- Analysing livestock network data for infectious disease control: an argument for routine data collection in emerging economies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Transmission Trees on a Known Pathogen Phylogeny: Enumeration and Sampling.Molecular biology and evolution · 2019Article
- Model diagnostics and refinement for phylodynamic models.PLoS computational biology · 2019Article
- outbreaker2: a modular platform for outbreak reconstruction.BMC bioinformatics · 2018Article
- PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.Molecular biology and evolution · 2018Article
- Incorporating genomic methods into contact networks to reveal new insights into animal behavior and infectious disease dynamics.Behaviour · 2018Article
- Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks.PLoS computational biology · 2017Article
- Overlap Extension Barcoding for the Next Generation Sequencing and Genotyping of Plasmodium falciparum in Individual Patients in Western Kenya.Scientific reports · 2017Article
- Using genomics data to reconstruct transmission trees during disease outbreaks.Revue scientifique et technique (International Office of Epizootics) · 2016Article
- Reconstructing transmission trees for communicable diseases using densely sampled genetic data.The annals of applied statistics · 2016Article
- Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set.PLoS computational biology · 2015Article
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7 authors.
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Abstract
There has been growing interest in the statistics community to develop methods for inferring transmission pathways of infectious pathogens from molecular sequence data. For many datasets, the computational challenge lies in the huge dimension of the missing data. Here, we introduce an importance sampling scheme in which the transmission trees and phylogenies of pathogens are both sampled from reasonable importance distributions, alleviating the inference. Using this approach, arbitrary models of transmission could be considered, contrary to many earlier proposed methods. We illustrate the scheme by analysing transmissions of Streptococcus pneumoniae from household to household within a refugee camp, using data in which only a fraction of hosts is observed, but which is still rich enough to unravel the within-household transmission dynamics and pairs of households between whom transmission is plausible. We observe that while probability of direct transmission is low even for the most prominent cases of transmission, still those pairs of households are geographically much closer to each other than expected under random proximity.
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